We have investigated the structure, function, evolution and immunogenic sites of the retinal S-antigen (48 K protein) and its gene. The complete amino acid sequences of human, bovine and murine retinal S-antigen have been determined by partial protein sequencing and cDNA sequencing. Coding sequences of S-antigen cDNAs from human, bovine and murine retinas have approximately 80% similarity. In contrast, noncoding sequences of these cDNAs have at most only 30% similarity. The polypeptide sequences of S-antigen from human, bovine and murine retinas are also very similar (-83%). Immunogenic sites of bovine S-antigen were determined, as were two monoclonal antibody binding sites (epitopes) and two uveitopathogenic sites (named M and K) using 20 different chemically synthesized oligopeptides. The minimum size required for EAU induction was also determined. M peptide was 12 and K peptide was 20 amino acids long. These small peptides contain all the necessary information for the induction of EAU. EAU was also observed following the adaptive transfer of T cell lymphocytes from Lewis rats which were previously immunized with M peptide, indicating that experimental autoimmune uveitis (EAU) induced by M was also a T cell mediated autoimmune response. The clinical and histopathologic features of EAU induced with M peptide were similar to those developed with native S-antigen. The M12 peptide of S-antigen from humans and mice has an identical sequence to that of bovine S-antigen. Searching the NBRF data bank revealed no extensive sequence homology between S-antigen and other proteins, although some sequence similarity was apparent with alpha-transducin. Interestingly, these include the sites subject to ADP-ribosylation by petussis toxin and the phosphoryl binding sites.